15 January 2003, which includes the civil districts of Ernakulam, Trissur and Palakkad of Kerala State and civil districts of Coimbatore and Thiruchirapally of Tamil Nadu. Most Rev. Thomas Mar Koorilos was appointed first Bishop of Muvattupuzha. The installation of Most Rev. Thomas Mar Koorilos and the official inauguration of the Eparchy took place on 6 February 2003.

Bishop Geevarghese Mar Timotheos submitted to the Holy See due to super-annuation on 29 March 2003 and the Holy See appointed Isaac Mar Cleemis, Auxiliary bishop of the Archieparchy of Trivandrum and of the Apostolic Visitor to Europe and America, as the Bishop of Tiruvalla. His Excellency Isaac Mar Cleemis was enthroned as the Bishop of Tiruvalla on 2 October 2003.

Most Rev. Joseph Mar Thomas was appointed as the Auxiliary Bishop of Trivandrum and Apostolic Visitor of North America and Europe on January 5, 2005. He was ordained Bishop by Major Archbishop-Catholicos Moran Mar Cyril Baselios on 19 February 2005 at St. Mary's Cathedral, Pattom, Trivandrum. During his Episcopal Ministry in the United States he acquired another house adjacent to Mar Ivanios Centre and was named as Mar Baselios Pastoral Centre. During this period four young students joined the seminary for priestly formation for the Syro-Malankara Catholic Missions in USA.

On 10 February 2005, a day engraved in golden letters in the history of the Syro-Malankara Catholic Church, His Holiness Pope John Paul II raised this Church to the status of a Major Archiepiscopal Church and appointed the then Metropolitan Archbishop as Major Archbishop of the Syro-Malankara Catholic Church through the Papal Bull Ab ipso Sancto Thoma. His Grace Pedro Lopez Quintana, the Apostolic Nuncio in India read the official declaration at St. Mary's Metropolitan Cathedral, Trivandrum. This was the crowning event of all the ecclesial communion endeavours since 1653. With this, the Malankara Catholic Church obtained a Synodal hierarchical structure with Major Archbishop as the "father and head" (pater et caput) of the Church exercising Patriarchal powers with the Synod of Bishops. In accordance with the provisions of the CCEO and the tradition of the Malankara Church, which has its roots in the Syro-Antiochene tradition, the Major Archbishop is the "Catholicos" of the Syro-Malankara Catholic Church, who with the Holy Episcopal Synod exercises Patriarchal powers envisaged in the CCEO (Pope Pius XII, Motu proprio, Cleri sanctitati, AAS 49 (1957) 430-603, c. 335). In complete concordance with this tradition, the pater et caput of the Syro Malankara Catholic Major Archiepiscopal Church assumed the title 'Catholicos' along with the title Major Archbishop.

The Faculty of Theology of St. Mary's Malankara Seminary got affiliated to the Pontifical Urbanian University, Rome, on 11 April 2005. The enthronment of Major Archbishop-Catholicos Moran Mor Cyril Baselios, as the Father and Head of the Syro-Malankara Catholic Major Archiepiscopal Church was on 14 May 2005. His Eminence Ignace Cardinal Mousa Daoud, the Prefect of the Congregation for the Oriental Churches presided over the liturgy of enthronement. His Grace Pedro Lopez Quintana, the Apostolic Nuncio in India, was present at the enthronement ceremony. The Malankara Major Archiepiscopal Curis (Catholicate Centre) started functioning at the St. Mary's Campus, Pattom, Trivandrum. On 20 May 2005 His Beatitude Moran Mor Cyril Baselios Catholicos blessed the Curia building. The Catholicos soon constituted the Holy Episcopal Synod. The first Synod of the Syro Malankara Catholic Church was convened from 16 to 18 August 2005 at the Major Archiepiscopal Curia ( Catholicate Centre), Trivandrum.

The first Holy Episcopal Synod constituted the Permanent Synod and the various Synodal Commissions headed by Bishops to take care of various Apostolates of the Church. The official bulletin, MALANKARA, is published from the Catholicate Centre, to communicate the Synodal acts and voice of the Syro-Malankara Major Archiepiscopal Church.

The Platinum Jubliee of the Reunion Movement and the Year of the Eucharist were celebrated jointly at Mar Ivanios Nagar, Punnamoodu, Mavelikara on 19, 20, 21 September 2005. His Grace Pedro Lopez Quintana, the Apostolic Nuncio in India, Shri Bhaironsingh Shekhawat, the Vice-President of India, and Sri Oommen Chandy, the Chief Minister of Kerala, participated in the celebrations.

As per the decision of the Second Holy Episcopal Synod and in consultation with the Holy See, the Major Archbishop-Catholicos established the Metropolitan Province of Tiruvalla with the Eparchies of Bathery and Muvattupuzha as suffragans on 15 May 2006 and Most Rev. Isaac Mar Cleemis was as the Metropolitan-Archbishop of Tiruvalla. Most Rev. Isaac Mar Cleemis was enthroned as the first Metropolitan-Archbishop of Tiruvalla on 10 June 2006.

According to the decision of the Holy Episcopal Synod of the Syro-Malankara Catholic Church, His Beatitude Moran Mor Cyril Baselios Catholicos erected the Eparchy of Mavelikara, bifurcating the Major Archieparchy of Trivandrum, on 1 January 2007. His Excellency Most Rev. Dr. Joshua Mar Ignathios, the Auxiliary Bishop of Trivandrum was transferred and was appointed the first Bishop of the Eparchy of Mavelikara. The Eparchy of Mavelikara comprises the presbyteral districts of Mavelikara and Kollam and parts of the presbyteral districts of Chengannur and Adoor. This includes with the civil districts of Alapuzha minus the portions that belong to the Archdiocese of Tiruvalla and parts of the civil districts of Kollam and Pathanamthitta.